PDB-3bzl: Crystal structural of native EscU C-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 3bzl

Title

Crystal structural of native EscU C-terminal domain

Components

(EscU) x 2

Keywords

MEMBRANE PROTEIN / PROTEIN TRANSPORT / Auto cleavage protein / Intein / T3SS / Type III secretion system

Function / homology

Function and homology information

dioxygenase activity / protein secretion / isomerase activity / plasma membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.71 Å

Authors

Zarivach, R. / Deng, W. / Vuckovic, M. / Felise, H.B. / Nguyen, H.V. / Miller, S.I. / Finlay, B.B. / Strynadka, N.C.J.

Citation

Journal: Nature / Year: 2008
Title: Structural analysis of the essential self-cleaving type III secretion proteins EscU and SpaS.
Authors: Zarivach, R. / Deng, W. / Vuckovic, M. / Felise, H.B. / Nguyen, H.V. / Miller, S.I. / Finlay, B.B. / Strynadka, N.C.

History

Deposition	Jan 18, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 22, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3	Feb 21, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bzl.cif.gz	61.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3bzl.ent.gz	45.7 KB	Display	PDB format
PDBx/mmJSON format	3bzl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3bzl_validation.pdf.gz	463.7 KB	Display	wwPDB validaton report
Full document	3bzl_full_validation.pdf.gz	466.2 KB	Display
Data in XML	3bzl_validation.xml.gz	11.8 KB	Display
Data in CIF	3bzl_validation.cif.gz	15.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bz/3bzl ftp://data.pdbj.org/pub/pdb/validation_reports/bz/3bzl	HTTPS FTP

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Related structure data

Related structure data	3bzoC 3bzpC 3bzrC 3bzsC 3bztC 3bzvC 3bzxC 3bzyC 3bzzC 3c00C 3c01C 3c03C C: citing same article (ref.)
Similar structure data	1wh4-d 6jmk-2 5ii9-1 2c6r-d 1rmd-d 2mbm-d 2yu4-d 3b71-2 5ii9-6 6tgt-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#131 - Nov 2010 Inteins similarity (1)

Deposited unit

A: EscU

C: EscU

B: EscU

D: EscU

hetero molecules

31 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: EscU

D: EscU

hetero molecules

defined by author&software
15.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: EscU

C: EscU

hetero molecules

defined by author&software
15.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	102.424, 55.121, 50.257
Angle α, β, γ (deg.)	90.000, 110.420, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	EscU Mass: 5991.751 Da / Num. of mol.: 2 / Fragment: UNP residues 215-262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EPEC E2348/69 / Gene: escU / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AJ26
#2: Protein	EscU Mass: 9480.065 Da / Num. of mol.: 2 / Fragment: UNP residues 263-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EPEC E2348/69 / Gene: escU / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AJ26
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Fragment: UNP residues 215-262 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Fragment: UNP residues 263-345 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.75 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: NaFormate, NaCl, Tris, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL11-1 / Wavelength: 0.97945 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 30, 2006

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97945 Å / Relative weight: 1

Reflection

Redundancy: 4.3 % / Av σ(I) over netI: 12 / Number: 35978 / R_merge(I) obs: 0.081 / Χ²: 1.79 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 8295 / % possible obs: 99

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.6	50	100	1	0.044	1.867	4.4
4.45	5.6	100	1	0.058	2.146	4.4
3.88	4.45	100	1	0.066	2.39	4.4
3.53	3.88	100	1	0.082	2.295	4.4
3.28	3.53	99.9	1	0.109	2.066	4.4
3.08	3.28	100	1	0.151	1.576	4.4
2.93	3.08	100	1	0.187	1.523	4.4
2.8	2.93	100	1	0.232	1.36	4.4
2.69	2.8	99.9	1	0.291	1.294	4.2
2.6	2.69	90.3	1	0.319	1.188	3.8

Reflection

Resolution: 1.71→50 Å / Num. all: 28254 / Num. obs: 27830 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / R_merge(I) obs: 0.056 / Χ²: 2.629 / Net I/σ(I): 19.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.71-1.78	5.2	0.355	2559	1.57	1	90.4
1.78-1.85	5.8	0.27	2721	1.78	1	98.6
1.85-1.94	6.1	0.199	2823	1.942	1	99.9
1.94-2.04	6.2	0.138	2803	2.197	1	100
2.04-2.17	6.1	0.104	2828	2.584	1	100
2.17-2.33	6.1	0.082	2813	2.902	1	100
2.33-2.57	6	0.072	2811	3.049	1	100
2.57-2.94	5.8	0.057	2842	3.241	1	100
2.94-3.71	5.4	0.048	2824	3.556	1	100
3.71-50	5.2	0.042	2806	3.409	1	96.7

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Phasing

Phasing	Method: SIRAS

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHELX		phasing
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
SHELXD		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 1.71→30 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.953 / SU B: 4.146 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.217	1406	5.1 %	RANDOM
R_work	0.187	-	-	-
all	0.188	28254	-	-
obs	0.188	27813	98.31 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 15.875 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.21 Å²	0 Å²	2.38 Å²
2-	-	-0.4 Å²	0 Å²
3-	-	-	0.85 Å²

Refinement step

Cycle: LAST / Resolution: 1.71→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1732	0	4	117	1853

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1798
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1228
X-RAY DIFFRACTION	r_angle_refined_deg	1.38	1.994	2439
X-RAY DIFFRACTION	r_angle_other_deg	1.181	3	3047
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.858	5	226
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.236	25	70
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.902	15	343
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.085	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	297
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1908
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	311
X-RAY DIFFRACTION	r_nbd_refined	0.245	0.3	332
X-RAY DIFFRACTION	r_nbd_other	0.199	0.3	1218
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.5	890
X-RAY DIFFRACTION	r_nbtor_other	0.097	0.5	922
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.209	0.5	140
X-RAY DIFFRACTION	r_metal_ion_refined	0.096	0.5	3
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.255	0.3	19
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.241	0.3	39
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.248	0.5	38
X-RAY DIFFRACTION	r_mcbond_it	1.017	2	1117
X-RAY DIFFRACTION	r_mcbond_other	0.276	2	445
X-RAY DIFFRACTION	r_mcangle_it	1.658	3	1823
X-RAY DIFFRACTION	r_scbond_it	1.256	2	691
X-RAY DIFFRACTION	r_scangle_it	2.023	3	609

LS refinement shell

Resolution: 1.71→1.759 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.286	84	-
R_work	0.225	1703	-
all	-	1787	-
obs	-	-	86.33 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.7147	1.3758	-0.4485	1.7443	-1.2301	2.94	0.0122	-0.1545	-0.1931	0.0854	-0.0144	0.0062	0.2068	0.0278	0.0022	0.1238	-0.0077	0.0246	0.1387	0	0.128	6.0753	2.9327	21.7853
2	25.0888	-5.9813	-6.647	4.6743	1.257	3.6538	0.0867	0.7005	0.0258	0.1082	-0.0918	0.3076	-0.0999	-0.3031	0.0052	0.0591	-0.0208	0.0773	0.1153	0.003	0.1207	2.0979	8.1926	16.5849
3	8.4944	1.1521	-4.5619	2.8853	-0.3616	3.703	-0.1315	-0.0085	-0.3949	0.1126	0.0161	-0.0628	0.1157	-0.0128	0.1154	0.037	-0.005	0.0204	0.0646	0.0178	0.0658	8.4629	4.6612	15.4108
4	4.7725	1.3052	-0.7693	8.0927	-3.6235	6.1819	0.2742	-0.5933	0.0871	0.6245	-0.1682	-0.0227	-0.2157	0.2136	-0.106	0.1669	-0.0157	0.0407	0.134	-0.0199	0.0503	6.995	7.1622	27.8769
5	3.8979	1.1849	3.4603	5.2369	4.2095	17.0066	0.1	0.0312	0.4503	0.1218	-0.044	0.4961	-0.8339	-0.6383	-0.056	0.075	0.0334	0.106	0.0485	0.0338	0.1897	1.1062	16.3128	14.1302
6	5.3085	-0.5876	-0.1833	3.4706	0.7399	3.9185	0.0268	0.4044	0.2518	-0.163	-0.0578	0.1085	-0.0164	-0.1925	0.0309	0.0169	-0.018	0.0236	0.1187	0.0163	0.0978	7.4021	9.6972	6.8891
7	14.4947	7.4243	4.7648	16.0644	-0.0375	22.69	0.5121	-0.839	0.975	1.2438	-0.7676	0.611	-0.3187	0.1622	0.2556	0.1264	-0.121	0.0724	0.1545	-0.0286	0.2424	16.165	16.738	18.9534
8	9.856	8.8197	8.9927	7.8924	8.0451	9.9167	-0.1574	0.1147	0.228	-0.1746	-0.0462	0.0772	-0.1369	0.1996	0.2036	0.2162	0.0418	0.0907	0.0948	-0.045	0.1796	27.9187	22.4704	-20.9192
9	3.3562	-0.3385	0.2056	2.3066	-2.0024	3.7186	-0.024	0.27	0.0656	-0.3127	-0.0136	-0.003	0.2353	-0.0255	0.0376	0.1184	-0.0043	0.0122	0.1172	0.001	0.1212	31.8547	23.4489	1.2145
10	7.9623	6.0467	-0.7428	7.2531	-0.8906	2.4437	-0.2009	0.3645	-0.073	-0.2071	0.1828	-0.2204	0.0561	0.1094	0.0181	0.0246	0.0088	0.0411	0.0971	-0.0024	0.1142	34.4681	19.7483	3.9338
11	7.0822	-3.6932	5.7854	5.0691	-6.0753	11.2364	-0.0597	0.0495	0.3208	0.187	0.0216	-0.1386	-0.4318	0.1197	0.0381	0.0334	-0.0059	0.0263	0.0576	-0.0257	0.0977	32.3236	29.4233	6.9759
12	10.4891	-5.9959	-3.3199	16.8977	6.7131	13.9425	-0.1112	-0.2379	-0.014	0.4282	0.1758	-1.0748	0.2435	0.8799	-0.0646	0.012	0.027	-0.0041	0.086	0.0001	0.217	41.7619	16.2481	12.1367
13	6.7062	0.8934	-2.7486	4.9234	-1.3412	13.9075	0.0308	-0.0618	-0.5908	-0.028	-0.0025	-0.6641	0.4832	0.2618	-0.0283	0.0475	0.0027	0.0067	0.0417	-0.0181	0.2465	34.5933	9.7965	7.9691
14	15.8902	-7.3314	1.4131	15.8751	-0.4978	5.2386	0.0652	-0.0877	0.033	0.2378	-0.0278	0.334	-0.0386	-0.1088	-0.0374	0.0749	-0.0424	0.0359	0.0864	-0.0053	0.0961	24.4695	19.8806	14.2739

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	245 - 262	37 - 54
2	X-RAY DIFFRACTION	2	C	B	263 - 271	1 - 9
3	X-RAY DIFFRACTION	3	C	B	272 - 294	10 - 32
4	X-RAY DIFFRACTION	4	C	B	295 - 305	33 - 43
5	X-RAY DIFFRACTION	5	C	B	306 - 314	44 - 52
6	X-RAY DIFFRACTION	6	C	B	315 - 335	53 - 73
7	X-RAY DIFFRACTION	7	C	B	336 - 343	74 - 81
8	X-RAY DIFFRACTION	8	B	C	209 - 244	1 - 36
9	X-RAY DIFFRACTION	9	B	C	246 - 262	38 - 54
10	X-RAY DIFFRACTION	10	D	D	263 - 294	1 - 32
11	X-RAY DIFFRACTION	11	D	D	295 - 309	33 - 47
12	X-RAY DIFFRACTION	12	D	D	310 - 318	48 - 56
13	X-RAY DIFFRACTION	13	D	D	319 - 330	57 - 68
14	X-RAY DIFFRACTION	14	D	D	331 - 344	69 - 82

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Yorodumi